Alignments for a candidate for BPHYT_RS34245 in Bradyrhizobium sp. BTAi1

GapMind for catabolism of small carbon sources

Alignments for a candidate for BPHYT_RS34245 in Bradyrhizobium sp. BTAi1

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= uniprot:B2T9V9
         (510 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  295 bits (756), Expect = 2e-84
 Identities = 183/478 (38%), Positives = 260/478 (54%), Gaps = 6/478 (1%)

Query: 14  VVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRF 73
           ++E   +TK FG+  AL DV   +  GE HAL+G NGAGKSTL+ ++TG+   D G VR 
Sbjct: 14  LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73

Query: 74  SGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDARA 133
           +G      + +DA    +A VYQ   ++ +LSVA+NL++ RQP R GV+    MRR A A
Sbjct: 74  AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHA 133

Query: 134 LLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRI 193
           LL  + +D+   A     SV  + +  IARA+   AR +ILDEPTA LD  E++ LFR +
Sbjct: 134 LLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVM 193

Query: 194 SELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGL 253
            +L  +G+  +F+SH L +VYEIC  VTVLR+ R I +  ++ LPR  LI  M G     
Sbjct: 194 RKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLDLIRMMLGRE--- 250

Query: 254 AVADAAARGALPADTA--VALELKELTGADYEG-VSFTVKRGEVVGLTGATSSGRTSVAE 310
                  R A   DTA  V +  K      Y       ++RGEVVGL G   SGRT  A 
Sbjct: 251 LAETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETAR 310

Query: 311 AIAGLRAAKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIA 370
            + G   A  G  SV G  +       +   G G  P++R  EG+V   +V EN  + + 
Sbjct: 311 LVFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQ 370

Query: 371 RVLGKFGIAAPAKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVL 430
              G     +  +++    + I  L I    PE  +  LSGGNQQK ++AR LAT+P +L
Sbjct: 371 ARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLL 430

Query: 431 VLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDDLRTCDRVLVMFRGRVAAE 488
           VL +PT G+DV +   ++ +V  + E+G A+LV+S ELD++ T    +V+ R R   E
Sbjct: 431 VLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVE 488



 Score = 77.8 bits (190), Expect = 9e-19
 Identities = 62/234 (26%), Positives = 103/234 (44%), Gaps = 6/234 (2%)

Query: 22  KRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAPSI 81
           K FG    +    + +  GE   L G  G+G++    ++ G  + D+GE   +G A    
Sbjct: 274 KGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARLVFGAERADSGEASVAGKAVRLN 333

Query: 82  ADRDAWRERVA-CVYQHST--IIRDLSVAENLFINRQPLRGGVIDWQAMRRDARALLDHW 138
           + RDA       C  +  T  I+ DL+V EN+ +  Q  RG         +D  A+    
Sbjct: 334 SPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQARRGLHRPLSRREQDEIAMRYIR 393

Query: 139 KIDVRE---DARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISE 195
            +D+R    +   G LS   +Q   +AR L+   + ++LDEPT  +D      + R + +
Sbjct: 394 MLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLLVLDEPTRGIDVGAHAEIIRLVRD 453

Query: 196 LQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGE 249
           L  +G+  L IS  L E+      V VLRD  H+      A+    ++ A+  +
Sbjct: 454 LCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEELKGDAVEVSSILAAIAAD 507


Lambda     K      H
   0.318    0.134    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 604
Number of extensions: 37
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 510
Length of database: 516
Length adjustment: 35
Effective length of query: 475
Effective length of database: 481
Effective search space:   228475
Effective search space used:   228475
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources